A spell that can’t be countered can still be targeted by spells or abilities that would counter it. The part of their effect that would counter the spell won’t do anything, but any other effects those spells or abilities may have will still happen, if applicable.

1/22/2016

There’s no functional difference between “can’t be countered” and “can’t be countered by spells or abilities,” but the latter is used for classes of spells that might require a target. Spells with targets can still be countered by the game rules if all of their targets become illegal before they resolve.